added slurm role and some refactorings

Author: jyotipm29

.gitmodules

@@ -1,20 +1,28 @@
-[submodule "galaxy/roles/galaxyproject.galaxyextras"]
-	path = galaxy/roles/galaxyprojectdotorg.galaxyextras
+[submodule "galaxy/ansible/roles/galaxyproject.galaxyextras"]
+	path = galaxy/ansible/roles/galaxyprojectdotorg.galaxyextras
 	url = https://github.com/jyotipm29/ansible-galaxy-extras
 	branch = 24.1
 
-[submodule "galaxy/roles/galaxy-postgresql"]
-	path = galaxy/roles/galaxy-postgresql
+[submodule "galaxy/ansible/roles/galaxy-postgresql"]
+	path = galaxy/ansible/roles/galaxy-postgresql
 	url = https://github.com/galaxyproject/ansible-postgresql
 
-[submodule "galaxy/roles/galaxy-tusd"]
-	path = galaxy/roles/galaxy-tusd
+[submodule "galaxy/ansible/roles/galaxy-tusd"]
+	path = galaxy/ansible/roles/galaxy-tusd
 	url = https://github.com/galaxyproject/ansible-role-tusd
 
-[submodule "galaxy/roles/galaxy-flower"]
-	path = galaxy/roles/galaxy-flower
+[submodule "galaxy/ansible/roles/galaxy-flower"]
+	path = galaxy/ansible/roles/galaxy-flower
 	url = https://github.com/usegalaxy-eu/flower-ansible-role
 
-[submodule "galaxy/roles/galaxy-redis"]
-	path = galaxy/roles/galaxy-redis
+[submodule "galaxy/ansible/roles/galaxy-redis"]
+	path = galaxy/ansible/roles/galaxy-redis
 	url = https://github.com/geerlingguy/ansible-role-redis
+
+[submodule "galaxy/ansible/roles/galaxy-repos"]
+	path = galaxy/ansible/roles/galaxy-repos
+	url = https://github.com/galaxyproject/ansible-repos
+
+[submodule "galaxy/ansible/roles/galaxy-slurm"]
+	path = galaxy/ansible/roles/galaxy-slurm
+	url = https://github.com/galaxyproject/ansible-slurm

galaxy/Dockerfile

@@ -91,18 +91,14 @@ RUN groupadd -r postgres -g $GALAXY_POSTGRES_GID \
     && apt-get -qq update && apt-get install --no-install-recommends -y software-properties-common gpg-agent curl sudo \
     && curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - \
     && add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" \
-    && sudo add-apt-repository ppa:natefoo/slurm-drmaa \
     && curl -fsSL https://research.cs.wisc.edu/htcondor/repo/keys/HTCondor-current-Key | sudo apt-key add - \
     && sudo add-apt-repository "deb https://research.cs.wisc.edu/htcondor/repo/ubuntu/current jammy main" \
     && apt-get update -qq \
     ## && apt-get purge -y software-properties-common gpg-agent \
     ## && apt-get install postgresql-10 --no-install-recommends -y \
     && apt-get install nginx-extras nginx-common --no-install-recommends -y \
     && apt-get install docker-ce --no-install-recommends -y \
-    && apt-get install slurm-client slurmd slurmctld slurm-drmaa1 --no-install-recommends -y \
-    && ln -s /usr/lib/slurm-drmaa/lib/libdrmaa.so.1 /usr/lib/slurm-drmaa/lib/libdrmaa.so \
     && apt-get install proftpd proftpd-mod-pgsql proftpd-mod-crypto --no-install-recommends -y \
-    && apt-get install munge libmunge-dev --no-install-recommends -y \
     && apt-get install nano --no-install-recommends -y \
     && apt-get install htcondor --no-install-recommends -y \
     && apt-get install git --no-install-recommends -y \
@@ -177,11 +173,10 @@ RUN chmod 0644 $GALAXY_CONFIG_DIR/reports.yml $GALAXY_HOME/ephemeris/sample_tool
 # Make python3 standard
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10
 
-ADD roles/ /ansible/roles
 ADD ansible/ /ansible/
 
 # Install ansible and related dependencies
-RUN apt update -qq && apt install --no-install-recommends -y software-properties-common dirmngr gpg gpg-agent \
+RUN apt update -qq && apt install --no-install-recommends -y software-properties-common dirmngr gpg gpg-agent bsdmainutils \
     && sudo add-apt-repository ppa:ansible/ansible \
     && apt install --no-install-recommends -y ansible \
     && apt purge -y systemd
@@ -209,28 +204,16 @@ RUN ansible-playbook /ansible/redis_provision.yml \
     --extra-vars redis_venv_dir=$GALAXY_VIRTUAL_ENV \
     --extra-vars redis_user=$GALAXY_USER
 
-# cleanup dance
-RUN apt purge ansible software-properties-common dirmngr gpg gpg-agent -y && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
-    && find $GALAXY_ROOT_DIR/ -name '*.pyc' -delete | true \
-    && find /usr/lib/ -name '*.pyc' -delete | true \
-    && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete | true \
-    && rm -rf /tmp/* /root/.cache/ /var/cache/* $GALAXY_ROOT_DIR/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm
-
-
-# Include all needed scripts from the host
-ADD ./setup_postgresql.py /usr/local/bin/setup_postgresql.py
-
-# Configure PostgreSQL
-# 1. Remove all old configuration
-# 2. Create DB-user 'galaxy' with password 'galaxy' in database 'galaxy'
-# 3. Create Galaxy Admin User '[email protected]' with password 'admin' and API key 'admin'
+# Install slurm
+RUN ansible-playbook /ansible/slurm_provision.yml \
+    --extra-vars galaxy_user_name=$GALAXY_USER
 
 RUN mkdir -p /shed_tools $EXPORT_DIR/ftp/ \
     && chown $GALAXY_USER:$GALAXY_USER /shed_tools $EXPORT_DIR/ftp \
     && ln -s /tool_deps/ $EXPORT_DIR/tool_deps \
     # Configure Galaxy to use the Tool Shed
     && chown $GALAXY_USER:$GALAXY_USER $EXPORT_DIR/tool_deps \
-    && apt update -qq && apt install --no-install-recommends -y ansible gpg gpg-agent g++ make bsdmainutils \
+    && apt update -qq && apt install --no-install-recommends -y g++ make \
     && ansible-playbook /ansible/provision.yml \
     --extra-vars galaxy_venv_dir=$GALAXY_VIRTUAL_ENV \
     --extra-vars galaxy_log_dir=$GALAXY_LOGS_DIR \
@@ -258,27 +241,36 @@ RUN mkdir -p /shed_tools $EXPORT_DIR/ftp/ \
     --extra-vars nginx_use_remote_header=True \
     --extra-vars tus_upload_store_path=$GALAXY_CONFIG_TUS_UPLOAD_STORE \
     --extra-vars gx_it_proxy_sessions_path=$GALAXY_CONFIG_INTERACTIVETOOLS_MAP \
-    --tags=galaxyextras,cvmfs --skip-tags=tusd,flower,redis -c local \
+    --tags=galaxyextras,cvmfs --skip-tags=tusd,flower,redis,slurm -c local \
     && . $GALAXY_VIRTUAL_ENV/bin/activate \
     && pip install WeasyPrint \
     && deactivate \
     # TODO: no clue why this is needed here again
     && cd $GALAXY_ROOT_DIR && ./scripts/common_startup.sh \
     && cd config && find . -name 'node_modules' -type d -prune -exec rm -rf '{}' + \
     && find . -name '.cache' -type d -prune -exec rm -rf '{}' + \
-    && cd / \
-    && rm $PG_DATA_DIR_DEFAULT -rf \
-    && python /usr/local/bin/setup_postgresql.py --dbuser galaxy --dbpassword galaxy --db-name galaxy --dbpath $PG_DATA_DIR_DEFAULT --dbversion $PG_VERSION \
-    && service postgresql start \
-    && service postgresql stop \
-    && apt purge gpg gpg-agent g++ make gcc -y && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \
+    && apt purge software-properties-common dirmngr gpg gpg-agent g++ make gcc -y && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* ~/.cache/ \
     # cleanup dance
     && find $GALAXY_ROOT_DIR/ -name '*.pyc' -delete | true \
     && find /usr/lib/ -name '*.pyc' -delete | true \
     && find /var/log/ -name '*.log' -delete | true \
     && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete | true \
     && rm -rf /tmp/* /root/.cache/ /var/cache/* $GALAXY_ROOT_DIR/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm
 
+# Include all needed scripts from the host
+ADD ./setup_postgresql.py /usr/local/bin/setup_postgresql.py
+
+# Configure PostgreSQL
+# 1. Remove all old configuration
+# 2. Create DB-user 'galaxy' with password 'galaxy' in database 'galaxy'
+# 3. Create Galaxy Admin User '[email protected]' with password 'admin' and API key 'admin'
+
+RUN cd / \
+    && rm $PG_DATA_DIR_DEFAULT -rf \
+    && python /usr/local/bin/setup_postgresql.py --dbuser galaxy --dbpassword galaxy --db-name galaxy --dbpath $PG_DATA_DIR_DEFAULT --dbversion $PG_VERSION \
+    && service postgresql start \
+    && service postgresql stop
+
 RUN touch /var/log/condor/StartLog /var/log/condor/StarterLog /var/log/condor/CollectorLog /var/log/condor/NegotiatorLog && \
     mkdir -p /var/run/condor/ /var/lock/condor/ && \
     chown -R condor: /var/log/condor/StartLog /var/log/condor/StarterLog /var/log/condor/CollectorLog /var/log/condor/NegotiatorLog /var/run/condor/ /var/lock/condor/

galaxy/roles/galaxy-flower renamed to galaxy/ansible/roles/galaxy-flower

@@ -0,0 +1,41 @@
+- hosts: localhost
+  connection: local
+  remote_user: root
+  vars:
+    slurm_roles: ['controller', 'exec']
+    slurm_config:
+      SlurmctldHost: localhost
+      SlurmUser: '{{ galaxy_user_name }}'
+      SelectType: select/cons_tres
+      SelectTypeParameters: CR_Core_Memory
+      StateSaveLocation: /tmp/slurm
+      ReturnToService: 1
+  roles:
+      - role: galaxy-repos
+      - role: galaxy-slurm
+  tasks:
+    - name: Install slurm-drmaa package
+      package:
+        name: slurm-drmaa1
+        state: present
+
+    - name: Create symbolic link for libdrmaa.so
+      file:
+        src: /usr/lib/slurm-drmaa/lib/libdrmaa.so.1
+        dest: /usr/lib/slurm-drmaa/lib/libdrmaa.so
+        state: link
+
+    - name: Setup tmp area for slurm
+      file: path=/tmp/slurm state=directory owner={{ galaxy_user_name }} group={{ galaxy_user_name }}
+
+    - name: Add script to update slurm configuration file
+      template: src=configure_slurm.py.j2 dest=/usr/sbin/configure_slurm.py mode=0755
+
+    - name: Setup Munge permissions and folder
+      file: path={{ item }} state=directory owner=root group=root recurse=yes
+      with_items:
+        - /var/run/munge
+        - /var/lib/munge
+        - /var/log/munge
+        - /var/run/munge
+        - /etc/munge